sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
7fd7402348aaf619358845d5f9c3ccc58edff516737ccf4fb088cab1ae405e68 | MATLAB | 965 | 40 | function meta=remove_line_index(meta,index)
% REMOVE_LINE_INDEX removes a line from the list of lines of the MetaBlock.
% META=REMOVE_LINE_INDEX(META,INDEX) removes the line in the specified
% index from the line-list of this metablock.
% If index exceeds the length of the list then the line is removed from the
% end ... |
18741773edc981c4d544056442311a8727b21c32ae9ddce8c330d0bc04da9c2b | MATLAB | 966 | 31 | classdef (Abstract) InputOutputDevice < handle
%INPUTOUTPUTDEVICE is a class for a generic i/o device.
% It is an observable class that signals 'DataReceived' events if it got
% input. 'DataReceived' events have an 'InputDeviceData' object with the
% properties 'pin' and 'value'. In that manner, it maps directly ... |
c8bacde88b0d2f29febe3ea9ab8efe41bff4cede79d0c6510cdc8f6b07cf8a82 | MATLAB | 966 | 21 | function [] = MIBItestBackgroundParameters_graded(reuseFigure)
global pipeline_data;
point = pipeline_data.points.get('name', pipeline_data.background_point);
countsAllSFiltCRSum = point.counts;
labels = point.labels;
capBgChannel = pipeline_data.capBgChannel;
t = pipeline_data.t;
gausR... |
e0acc31b310571dc87c4c04f86050a05bdb8228cf3aa27220cc1566c666cfcdc | MATLAB | 966 | 17 | %-----------------------------------------------------------------------
% Job saved on 19-Feb-2020 16:30:55 by cfg_util (rev $Rev: 7345 $)
% spm SPM - SPM12 (7487)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
function matlabbatch=spm_func2atlas_normaliza... |
c05f813fbf7743f9871766365bde25241e982b969c8acf1341843359a2916de8 | MATLAB | 967 | 36 | function rpx_str=get_rpx_string(sig)
% GET_RPX_STRING returns part of the relevant rpx file name according to the
% signal and envelopes that are defined for the signal coordinator.
% The part of the file name is of the form :
% _<signal-name>_<env1-first-letter><number-of-such-env>
% For example : str= '_FRQ_M3' -----... |
3d9976598b5801061a21f80849bf9f7e8fe2b4f0f72069f1104735916dff3003 | MATLAB | 970 | 30 | function comp= change_sweep_param(comp,varargin)
% change_sweep_param(sig_comp, field_name1, val1, field_name2, val2...)
% changes sweep's fields to the given values.
% Sweep fields are: Sdata, Sdata_formula, Edata, Edata_formula, Num_data,
% Num_data_formula, Reps, Reps_formula, Mode, Step.
param_argin = varargin;
... |
af0b4008b417a1393c26cc6b24ff0cea9fb0c3928f624dcb95d548730b12eab4 | MATLAB | 971 | 20 | %-----------------------------------------------------------------------
% Job saved on 27-Feb-2020 20:55:45 by cfg_util (rev $Rev: 7345 $)
% spm SPM - SPM12 (7487)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
%%
function matlabbatch=spm_realign_estimate(Dir_a... |
413562829e2a353038636f4c7fb78fc39fc8e0beadc0c027e530c7c47d78fc12 | MATLAB | 972 | 32 | function val = get(env,prop_name)
% GET Get Envelope property from the specified object
% and return the value. Property names are:
% Name, Signal, Num_of_comps, Comp_list, Comp_list_str,ENVELOPE_NAMES, ENVELOPE_NUMBER.
if isa(prop_name,'char')
index=strmatch(prop_name,env.comp_list_str,'exact');
if ~isempty(... |
4923b05ff036299ebcf2f1faca7ac1e68033c4a68755dc070945c62067bfc70e | MATLAB | 972 | 41 | function type = IdentifyType(toReward)
switch toReward.beamind
case 1 %infood1
type = 1;
chanid = 'Port1/Line0:0';
case 2 %inwater1
type = 2;
chanid = 'Port1/Line2:2';
case 3 %infood2
type = 1;
chanid = 'Port1/Line1:1';
case 4 %inwater2
type = 2;
... |
4d7596de9262d4893de55f9eb6f2678974c089ae8f6976596d21c3cded73dfdd | MATLAB | 972 | 30 | function [centroidDist] = centroidDist(obj,clusters,nCluster,useChans,maxDimension)
%centroidDist Euclidean distance between centroids
% clusters = Integer indices identifying clusters
% nCluster = Number of clusters overall
% useChans (optional) = logical array of channels to use
% maxDimension (optional)... |
a55bd8242cecc9b112cc9a4379a82d994b86735991de6d0b4d99dadf43820b8b | MATLAB | 974 | 27 | function printFields(level, obj)
fields = fieldnames(obj);
for i=1:numel(fields)
field = getfield(obj, fields{i});
try
if isstruct(field)
disp([repmat(' ',1,level*3), fields{i}, ': {'])
printFields(level+1, field)
disp([repmat(' ',1,lev... |
dd882952c939a5e79d4eb27f55e0835e8a5c86717766f340c65286c790e4a7fc | MATLAB | 975 | 25 | function arduinoPorts = findArduinoPorts()
%FINDARDUINOPORTS find COM-ports auf connected Arduino devices
% This function returns a cell-array of strings with all Arduino
% COM-ports that could be found on the computer.
%
% Attention: This function is platform dependent and works on Windows
% only. It depends o... |
a63e0c7a5fe152bd0280dd165f6754dd76ef06da9dd0f2ca66e4e36a81818f93 | MATLAB | 977 | 30 | function [ pendantPair ] = PendentPair( F, index, ind )
%% [ pendantPair ] = PendentPair( F, index, ind )
%%
%% This function is the core sub-routine of the QueyranneAlgorithm.m
%%
%% First written by Shohei Hidaka Oct 22nd, 2015.
%% Revised (added its description in comments) by Shohei Hidaka Jan 13th, 2016.
%%
%... |
e615bd4760e561a5c9c54d623218980fa7ad9f82da7d317dfbc69cc3a43487ef | MATLAB | 977 | 37 | function [points] = tcp_server()
h = tcpip('localhost',80,'NetworkRole','server');
% Wait for connection
disp('Waiting for connection');
h.InputBufferSize = 6;
fopen(h);
flag = true;
points = [];
disp('gone into loop')
while flag
if(h.BytesAvailable)
data = fread(... |
76bc51ea30a7c321b7c1bc2deb2b6e96a4471c0b8ee5d69c8761e9bbe4a62cda | MATLAB | 982 | 36 | function p_m = marginalize(p,index,N,N_st)
% ---------------------------------
% PURPOSE: marginalize probability distribution p(X)
% Input
% p: probability distribution of X
% index: marginalized out other variables than those indicated by index
%
% Output
% p_m: marginalized probability distribution
%---------------... |
75925cb484931fd36d7ff17e6a5c2b1355db90fa47691c046b1e740e1baa5d17 | MATLAB | 989 | 28 | function flank=FLANKING_BAND_CO(varargin)
% FLANKING_BAND class constructor.
switch nargin
case 0
% if no input arguments, create a default object
m_sig=Main_signal('FLANKING_BAND_CO');
flank.num_of_comps=6;% FLANKING_BAND has 2 more unique components beside the basic 4.
% load filtercoefficients
load(... |
271959d35b5a03ccc9a4a00e5235fc6c78a51805b192d0244a8d395c3aec7d47 | MATLAB | 991 | 36 | function lgd = plot_short_time_wrapper(t_axes, pinfo, param, zones)
fname = sprintf('metadata_%04d-%02d-%02d_rat-%02d', pinfo.Year, ...
pinfo.Month, pinfo.Day, pinfo.Rat);
S = load(fullfile('..', 'data', fname));
metadata = S.metadata;
[loc, trial] = get_defined_data(pinfo.Year, pinfo.Month, ...
pinfo.Day,... |
b1161afdf659f36dfdc05d65c6e1789d66eb7e3243b7be8b315c423ae898e62f | MATLAB | 991 | 36 | function [Xrec, shearletSystem] = MIRO_Shearlet_thresholding(X,Var,shearletSystem,thresholdingFactor,mode,smp,tophat)
% Shearlet decomposition, microlocal thresholding and reconstruction
%% Shearlet decomposition
coeffs = SLsheardec2D(X,shearletSystem);
%% Shearlet shrinkage
switch mode
case 's'
... |
2d68011a2a64e6867eb5cc1ee34bebad9788ed678dc8fc25aa26631a1da27fd2 | MATLAB | 993 | 31 | %BLED Black to red variation of the hsv colormap
%
% Examples:
% map = bled;
% map = bled(len);
% B = bled(A);
% B = bled(A, lims);
%
% A variation of MATLAB's hsv colormap, which starts in black and gradually
% increases in color saturation.
%
% The function can additionally be used to convert a re... |
74f82f9afffeefd6b08cc4c37f1b9f98c07bed632bb382cd8c88204060db9c6f | MATLAB | 993 | 31 | %WHED White to red variation of the hsv colormap
%
% Examples:
% map = whed;
% map = whed(len);
% B = whed(A);
% B = whed(A, lims);
%
% A variation of MATLAB's hsv colormap, which starts in white and gradually
% increases in color saturation.
%
% The function can additionally be used to convert a re... |
f7cb78a0e4c557106179db21760d76816a3acf66aaa7e1d0662254db99ac97d4 | MATLAB | 995 | 28 | function flank=FLANKING_BAND_IND(varargin)
% FLANKING_BAND class constructor.
switch nargin
case 0
% if no input arguments, create a default object
m_sig=Main_signal('FLANKING_BAND_IND');
flank.num_of_comps=6;% FLANKING_BAND has 2 more unique components beside the basic 4.
% load filtercoefficients
loa... |
339ce7c3acbe984d86e71bfa805199861599908c96a220206a3482a06ed9ff0b | MATLAB | 996 | 32 | function p = add_lines(ax, trials, start_time, zones, do_port_positions, time_colors)
% JN 2020-07-02
lw = 2;
if do_port_positions
for i = 1:6
plot(ax, [-1 trials.t_fdb(end) + 2 - start_time], ...
[1 1] * zones.AngleCenter(zones.AreaNum == i), 'color', ...
[.8 .8 .8 .5]);
%t... |
bbf954d12cd249fd533393fb815724d72e37b4befb25d40c7b4b5e02cc3af8c4 | MATLAB | 996 | 28 | function [counts, labels, tags] = loadTIFF_folder(path)
% First we look for all TIFF files in the given path
fileList = [dir(fullfile(path, '*.tiff'));...
dir(fullfile(path, '*.tif'))];
if isempty(fileList)
error(['No TIFF files found in ', path]);
end
files = {fileList.name}';
r... |
6f3c7d764ccfe94de0c1e77b38b88cb9b5bf9818fac24812f1a8c79c72129de0 | MATLAB | 997 | 32 | function saveTIFF_mibi(opts)
fields = fieldnames(opts);
argstring = '';
for i=1:numel(fields)
field = fields{i};
arg = num2str(opts.(field));
if isnan(str2double(arg))
if contains(arg, ' ')
arg = ['"', arg, '"'];
end
else
ar... |
a3b95e8233d34024fb7283f6e54bcf941bb1bffc40a9dbf3675b0622fca31f73 | MATLAB | 997 | 47 | function MOV_DATA=fb_motion_correct(MOV_DATA,TEMPLATE,varargin)
%motion corrects the data in MOV_DATA to match a template image using xcorr
%
%
%
upsample_factor=100;
nparams=length(varargin);
if mod(nparams,2)>0
error('Parameters must be specified as parameter/value pairs');
end
for i=1:2:nparams
switch lower(va... |
13a9733c9db92a34abf5a2a0ca43dd55374a38934ed4b1d86ea065fe44bb196c | MATLAB | 1,000 | 42 | function [areaTable, centData] = setFuncArea(inputvector)
loclen = inputvector(1)-3;
locx = inputvector(2:loclen/2+1);
locy = inputvector(loclen/2+2:loclen+1);
x0 = inputvector(loclen+2); % center x
y0 = inputvector(loclen+3); % center y
R = inputvector(loclen+4); % radius
centData = [x0 y0 R];
r1 = R/8;
r2 = 3*R/8; ... |
df3c4b633492bbabfb92a28d197011c0542f9bb644b3087a14b65f6ef4c28598 | MATLAB | 1,001 | 25 | function PERFORMANCE_surrogate=get_classification_performance_surrogate(real_type,pred_type,n_surrogates)
% markov chain permutations of predicted type
[n_per_type,transitions_abs]=count_transitions(real_type);
%exclude states that do not occur
transitions_abs=transitions_abs(n_per_type~=0,:);
transitions_abs=... |
1f401a3139a24f5f4eb63c6cd63a832410bac642eb26d369bb6b1d67f606ac45 | MATLAB | 1,003 | 32 | function bw=adaptivethreshold(IM,ws,C,tm)
%ADAPTIVETHRESHOLD An adaptive thresholding algorithm that seperates the
%foreground from the background with nonuniform illumination.
% bw=adaptivethreshold(IM,ws,C) outputs a binary image bw with the local
% threshold mean-C or median-C to the image IM.
% ws is the ... |
2a2ac6e044402b63d93c1d39af37bb9ded3af5a098dfcb61e11680908cd4ca99 | MATLAB | 1,003 | 31 | function out=set_trial_data(out,data,trial_index)
for electrode=1:out.num_elec
% for electrode=1:2
if out.LFPmask(electrode)
chan_data=data{electrode};
len=length(chan_data);
if len>0
% tmp=zeros(1,len);
% tmp(1:len)=chan_data;
out.trial_data{trial_ind... |
c5143225d25006d2feecb0697a56b6efe71b1f06a632c026ed84395274d904f6 | MATLAB | 1,005 | 36 | function h = mctrans(b,t)
% MCTRANS McClellan transformation
%
%
% H = mctrans(B,T) produces the 2-D FIR filter H that
% corresponds to the 1-D FIR filter B using the transform T.
%
%
% Convert the 1-D filter b to SUM_n a(n) cos(wn) form
%
% Part of the Nonsubsampled Contourlet Toolbox
% (http://www.mathworks.de/ma... |
5aa42f4ab64760753fad49b160588951888fc101d3f94240a83635d20c6b8447 | MATLAB | 1,006 | 30 | function R = mRespIndividual(gain, direction, PD, sigD, sponR, cparams1, cparams2, cparams3, cparams4)
% gaussian shape tuning curve
% direction = stimulus dir
% sigD = tuning width
% pd range: -180 ~ 180
if PD > 180
PD = PD - 360;
end
if PD < -180
PD = PD + 360;
end
% degree to radian
dirD = (direction - PD)*pi/18... |
adb005d863dc5511d7629f57da505b34109248a3d0fcc269e5a690049505b4f3 | MATLAB | 1,007 | 38 | function meta=add_line_index(meta,line,index)
% ADD_LINE_INDEX adds a line to the list of lines.
% line_list of this metablock in the specified index.
% META=ADD_LINE_INDEX(META,LINE,INDEX) adds the given line to the
% line_list of this metablock in the specified index.
% If index exceeds the length of the list then t... |
e7e29bb962730efb466e3a4fe2ba33323fcea6d925e20e9e1e40e6ff2c561f16 | MATLAB | 1,007 | 30 | function comp= change_sweep_param(comp,varargin)
% change_sweep_param(sig_comp, field_name1, val1, field_name2, val2...)
% changes sweep's fields to the given values.
% Sweep fields are: Sdata, Sdata_formula, Edata, Edata_formula, Num_data,
% Num_data_formula, Reps, Reps_formula, Mode, Step.
param_argin = varargin;... |
160ad66128da9efe0ee17103de7dfba8374ee2966f469dcf78dfa3a78037c426 | MATLAB | 1,011 | 30 | function comp= change_sweep_param(comp,varargin)
% change_sweep_param(sig_comp, field_name1, val1, field_name2, val2...)
% changes sweep's fields to the given values.
% Sweep fields are: Sdata, Sdata_formula, Edata, Edata_formula, Num_data,
% Num_data_formula, Reps, Reps_formula, Mode, Step.
param_argin = varargin;... |
a4686326d1669635a4088803dba2708d03bf4a9070fa86b2394f1314c563cc76 | MATLAB | 1,011 | 22 | load("timeseries.Yeo2011.mm316.mat");
for m = 1:316
subject_mx645 = corrcoef(transpose(subjects(m).mx645));
subject_mx1400 = corrcoef(transpose(subjects(m).mx1400));
subject_std2500 = corrcoef(transpose(subjects(m).std2500));
subject_mx645(24,:) = [];
subject_mx645(:,24) = [];
subject_mx1400(24... |
a46d47a7d403b722fca33e632465ea5c16c426d7abdd7157eb585586bf4b34ad | MATLAB | 1,014 | 22 | function [event_timing_struct, t_behavior] = load_behavior(rat_dir)
% Function load_behavior() reads the beh_struct_for_RIFF_player.mat that is produced by the pipeline.
%
% Inputs:
% rat_dir - (str) - Location of the beh_struct_for_RIFF_player.mat, inside the experiment folder
%
% Output... |
d6aceb499f76e2d31aa4c270dcb50551ea5f094c572ad682eaed1c5297f2575e | MATLAB | 1,014 | 28 | function write_tiff_folder(counts, labels, path)
path = strsplit(path, '.'); path = path{1}; % normalizing name
tiff = Tiff([path, '.tiff'], 'a');
for index=1:numel(labels)
setTag(tiff, 'PageName', labels{index});
setTag(tiff, 'SubFileType', 0);
setTag(tiff, 'Photometric', 1);
... |
02b6bd2902aa5daec1addcf16be549bc82310cd2450b4554a338c3ba617e33e3 | MATLAB | 1,016 | 27 | function samp_points=synth(sig,samp_rate,trial_dur,varargin)
% SYNTH is NEW_SIGNAL synth function.
% SAMP_POINTS=SYNTH(SIG,SAMP_RATE,TRIAL_DUR,VARARGIN) Samples the signal
% according to the givan SAMP_RATE and TRIAL_DUR. Returns the sampled
% points.
% varargin holds the requested Frequency value and the requested Ph... |
dd6d27e5bdc706337b6c64a0f0b6ebc993b5ed7ac0c1550995126fb094e96a39 | MATLAB | 1,016 | 40 | function [I_CaL, df_L, dd_L] = L_type_Ca(V, d_L, f_L)
g_CaL = 2.1;
E_CaL = 50;
if(abs(V + 45) < 0.0001)
alpha_d_l = 16.72.*2.5 - 50.0.*(V + 10)./(exp(-(V + 10)./4.808) - 1);
elseif(abs(V + 10) < 0.0001)
alpha_d_l = -16.72.*(V + 45)./(exp(-(V + 45)./2.5) - 1) + 50.*4.808;
else
alpha_d_l = -16.72.*(V + 10 ... |
ca841300436496f1b5fa65adaa90ac15a975ffcb33966476be37dfa6fdee4079 | MATLAB | 1,017 | 31 | function J=thresholdImage(I,NThresholds)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% INPUTS : I is the input image
% NThresholds is the number of thresholds required. NThresholds
% lies between the 1 and (the difference between the maximum and
% minimum graylevel prese... |
391a708feaed7ec66cc2f84015534464a7899885d36674b3b3c32863379f7ade | MATLAB | 1,019 | 34 | function [start_trial_points,stime_points]=generate_timing_points(handles,line,trial_dur,circuit_samp_rate)
% samp_rate=get(line,'Samp_rate');
stimlist = handles.stimlist;
samp_rate=stimlist.T{line,'samp_rate'};
% minimum_stime=get_least_stime(line);
minimum_stime = stimlist.T{line,'stime'};
num_points=ceil(samp_rate... |
407cd7b311589dcb2e85c3aba3ea7cf394d7d65daf364e3be3cbec17f2bf09b6 | MATLAB | 1,019 | 49 |
%% calculate the mean angle of the right most cluster
cmap = parula(11+1);
cmap = cmap .* repmat([.9 .8 .9],size(cmap,1),1);
thresh = 10;
x = obs2obs(:);
y = exe2obs(:);
ind_min_rel = x>=thresh;
x = x(ind_min_rel);
y = y(ind_min_rel);
% convert to angle
angle = atand(y./x);
n = sum(~isnan(angle));
nbins = round... |
df03b3bdc88da708fe3ff7c2648b1660de57e309cc1ab63217fcfcb49614e372 | MATLAB | 1,021 | 36 | function p_m = marginalize_table(p,index,N_st,sigma_table,pow_vec)
% ---------------------------------
% PURPOSE: marginalize probability distribution p(X)
% Input
% p: probability distribution of X
% index: marginalized out other variables than those indicated by index
%
% Output
% p_m: marginalized probability distri... |
4cd48740ff307299ea12554662e17f6b05bc95d2ac90850f11253492b5bbda9c | MATLAB | 1,023 | 29 | function stats = getSessionStatsFromLog(el, headerStr, trialFilter)
%GETSESSIONSTATSFROMLOG computes session statistics from an eventLog.
% Arguments:
% el - eventLog of a LogBook
% headerStr - the field name of the trial struct that identifies the
% grouping factor
% trialFilter - optional: a function ha... |
6c3dd83e2d3b72a6ffc235cd39befe6562d5e05be3924856a5c47489d82d9e99 | MATLAB | 1,026 | 27 | function sig= change_sweep_param(sig,comp,varargin)
% CHANGE_SWEEP_PARAM changes sweep's fields of the given component to the given
% values and returns the updated signal.
% sig=CHANGE_SWEEP_PARAM(SIG,COMP,FIELD_NAME1,VAL1,FIELD_NAME2,VAL2,...)
% changes sweep's fields of the given component to the given values and
% ... |
c5504ff1d702d3d82606967896e6bf411462325d6e1735e0f9c5b809bc98d521 | MATLAB | 1,026 | 41 | function asynchSound(q)
send(q,'start');
qout=parallel.pool.PollableDataQueue;
send(q,qout);
fs = 192000;
dev = audioDeviceWriter;
dev.Driver = 'ASIO';
dev.Device = 'ASIO MADIface USB';
dev.SampleRate = fs;
dev.ChannelMappingSource = 'Property';
dev.ChannelMapping = 1:14;
dev.SupportVariableSizeInput = true;
dev.Buffer... |
7ec90a341e0e56369f66fe23864cd2146c5efdf237d3537c55e33bf491fbea18 | MATLAB | 1,027 | 41 | function m_sig=remove_envelope_index(m_sig,index)
% REMOVE_ENVELOPE removes an envelope from the list of envelopes of a Main signal.
% M_SIG=REMOVE_ENVELOPE(M_SIG,INDEX) removes the envelope in the specified
% index from the list of envelopes of the given Main signal.
% If index exceeds the length of the list then the... |
9f5238606dc3975d571f4d5b170344b36766cbc7a789d491f14bd6c681d85e10 | MATLAB | 1,028 | 32 | % Create a function to smooth data right before interpolation
% Updated: August 30, 2022
function [dendSmooth,dendSmoothIdx] = NeurSmoothData(dendId,dendSkel2,sFactor)
% Initialize
dendSmoothIdx = dendId;
dendSmooth = zeros(size(dendSkel2));
% Find NaN values or values less than 1 (out of bounds)
... |
dd8ed0d3c35b14ceae8e6b8644115c34adef8747776c1fa78e3e1f224c2ee042 | MATLAB | 1,029 | 17 | function writeTriByu(filename, triangles, vertices)
% writeTriByu(filename, triangles, vertices)
% Writes a triangular mesh to BYU format
% filename - path to BYU file to create
% vertices - Mx3 matrix of vertex coordinates
% triangles - Mx3 matrix of indices into the vertices matrix
dlmwrite(filename, [1 size(vertices... |
fa95f3c9b20cd9577715fd4804f4562e4536a3c6584fc8490c1865878d930ab3 | MATLAB | 1,031 | 32 | %%
% This function generates n random numbers that are integers
% between rand_min and rand_max.
% The distribution of these random variables is like a Gaussian
% distribution with mean mu and std sigma, but rounded to the nearest
% integer and wrapped around the interval [min,max].
%%%
function [ z ] = CircRandNfu... |
95b0b183496a0cdb7afe7b44a241aaf77807dc55a5863afeb44a7d3a66e8db77 | MATLAB | 1,032 | 29 | function [electrodeTable,ROImap] = loadROItable(useSheet,mapping)
%loadROItable Loads the ROI table.
% Detailed explanation goes here
if nargin<1
useSheet = 'ROI_table';
end
dataPath = getLocalPath('ECoGmeta');
electrodeFilePath = [dataPath filesep 'ROITable' filesep];
orig_s... |
05e21766866170ba9ee2209b06911163647ff1bb0053c8bf3c074eb871c67ef3 | MATLAB | 1,036 | 41 | function [CROPPED,TM] = cropDATA(DATA_fulltm,sdftm,sdfwin)
if size(DATA_fulltm,3) > 1
error('cropping only works on one dimensional stimulus. In the past we had "padrows"')
disp('archived')
disp(' padrows = repmat(pad,size(condition,1),1); % pads with NANs if you are not in that condition any more. ')
... |
18e03cd33cd32f9412072cdddf757009e9ee45bb3c3b520723633252a93424c5 | MATLAB | 1,037 | 31 | function stateTransition_plot_FigS6(theHbT,theEMG,theLFP,specT,specF,theTitle,plotTime,plotNum)
titles={'Quiescent Awake to Quiescent Asleep','Quiescent Asleep to Active Asleep','Quiescent Awake to Active Asleep',...
'Active Awake to Active Asleep','Quiescent Asleep to Active Awake','Active Asleep to Active Awa... |
0aa161c1c72ae1b00759565f0bdd058dfa944c22a6a638125723428ff5c35476 | MATLAB | 1,041 | 34 | function m_sig=add_envelope_index(m_sig,env,index)
% ADD_ENVELOPE_INDEX adds an envelope to the given Main-Signal list of
% envelopes.
% M_SIG=ADD_ENVELOPE_INDEX(M_SIG,ENV,INDEX) adds the given envelope (ENV) to the
% envelope list of this Main-Signal(M_SIG) in the specified index
% If index exceeds the length of the ... |
bb3255cb765639c5323dc045d95dc6a850f8166fdfa4539be4b0ddde03acb2a8 | MATLAB | 1,041 | 24 | function ExVivo_Setup_FromDiffusion(path)
%% Changing path names from Sebastian's data:
clc;
load(fullfile(path,'Chiasm1_allecho','Image_lists_R2s_1stO.mat'));
%figure;
for indx = 1:16
[pthname, fname, ext] = fileparts(Porg{indx,1});
new_pthname = fullfile(path,'Chiasm1_allecho',num2str(indx));
fn... |
a6a793e987883db4ded754aed64509ae7117322e9d14fe749fc557c34221b8c4 | MATLAB | 1,043 | 31 | function plot_consecutive_bars(data, ylabel_string, ylimit)
number_subjects = size(data,1);
figure
ax = axes;
bar(1, mean(data(:,1)), 'k');
hold
bar(2, mean(data(:,2)), 'r');
bar(3, mean(data(:,3)), 'b');
bar(4, mean(data(:,4)), 'g');
%Plot confidence intervals
for i=1:size(data,2)
plot([i,i], [mean(data(:,i))-s... |
879ce0799cc4cec951f16e1ff524145ba3929276a7b94f753da65b7c3adcbf78 | MATLAB | 1,045 | 32 | function env_counter_arr=get_num_spec_env(sig)
% GET_NUM_SPEC_ENV returns an array that specifies the number of envelopes
% of each kind on the specified signal.
% ENV_COUNTER_ARR=GET_NUM_SPEC_ENV returns an array that specifies the number of envelopes
% of each kind on the specified signal.
% First cell represents MTF... |
b576c69dca9de6007c136f018b36d32432f56f70b391a8e2560eb2a399cacf64 | MATLAB | 1,049 | 37 | function [...
dSL, dA, dTT, dU, dV_e, Force, dO_TnCa...
] = force_generation(V_e, SL, TT, A, U, data, Ca_i, ATP_i, ADP_i)
F_kl = data.F_kl*5000;
Ff = data.Ff;
F_go = data.F_go;
F_gl = data.F_gl;
SL_0 = data.SL_0;
N_c = data.N_c;
F_k0 = data.F_k0;
F_k1 = data.F_k1;
FN = data.FN;
F_k05 = data.F_k05;
k_XBATP = da... |
3611ac2836fdc59c5bd8b6fe7bf97ee16146cbf596f82d55d4779bb4122ac21a | MATLAB | 1,052 | 30 | function list=get_comp_list(main_sig,external_comp)
% GET_COMP_LIST returns the list of components of a Main_signal object.
% LIST=GET_COMP_LIST(MAIN_SIG) returns the list of components of a
% Main_signal object including components that are part of it's Envelopes.
% LIST=GET_COMP_LIST(MAIN_SIG,EXTERNAL_COMP) returns... |
a58788ce3c240f511e3bb56019c3dadbc4a87db32d7d6a348229f7345481eb11 | MATLAB | 1,052 | 26 | function [Result,arraydata,realDataSizeWords] = AO_GetNextBlock(sizeOfArrayWords)
%% Function used to get the nex new block data coming from the embedded
%sizeOfArrayWords :The max size of data the array can contain
%arraydata :Pointer to an array to hold the new data ,the data contain stream format in ord... |
a150c16a736edbb4754a4e209d507ef31d5767c670eda4366436747107e5e6c8 | MATLAB | 1,053 | 48 | function beam_ind = InputBeams()
s = daq.createSession('ni');
addDigitalChannel(s,'Dev1','Port0/Line0:3','InputOnly')
addDigitalChannel(s,'Dev1','Port2/Line0:3','InputOnly')
addDigitalChannel(s,'Dev1','Port4/Line0:3','InputOnly')
data=inputSingleScan(s);
while sum(data) == length(data)
data=inputSingleScan(s)... |
216a9997ea72d74f330a30ab5a0f9159dcdbf64abf2f2e02057cbb65361236a7 | MATLAB | 1,058 | 36 | % GET_RELATIVE_LOCATION returns the relative location of the given value
% within the range of possible values of the given component.
% LOC=GET_RELATIVE_LOCATION(COMP,COMP_VAL) returns the relative location of
% the given value (COMP_VAL) within the range of possible values of the
% given component (COMP).
function l... |
ff62174d76b835e846c0d20fb185e886e922dd1d8b367372a1a6f12cfd67f154 | MATLAB | 1,060 | 26 | function mapIntensityOnSurf (in_subj_surf_byu,in_qmri_nii, out_qmri_txt, out_qmri_surf_vtk)
%in_subj_surf_byu='~/graham/scratch/test_surfmorph/surfmorph_dev/work/iter1/sub-CT01/propSurface_subjspace_nii.byu'
%in_qmri_nii='~/graham/scratch/test_surfmorph/surfmorph_dev/work/sub-CT01/labels/t1/probseg/striatum_cortical.n... |
e45b351c1d1ad6a0c7ac747c920d0d271b42310bfce0d70835794474553a683e | MATLAB | 1,066 | 41 | function dataForJASP = jasp_2x2_RESP(IDX)
%% Goal
% use gramm and plot the simultaneous congruent, incongruent, and monoc
% preferred.
% line plots using "methods for visualizing repeated trajectories"
%% Initial variables
conditNameForCC = IDX.allV1(1).condition.Properties.RowNames;
TM = IDX.allV1(1).TM(1:560);
cle... |
f6ad5301dc99d1bd6da15cd6085f20cd2ca0c485b3f58f0e1184527759351bc8 | MATLAB | 1,067 | 42 | function [res_pa5,succeeded,err]=reset(pa5)
dev_num=get(pa5,'Device_num');
err='';
actx_cntrl=get(pa5,'Controler');
dev_num=get(pa5,'Device_num');
res_pa5=NaN;
% if (invoke(actx_cntrl,'ConnectPA5','GB',dev_num)==0)
% if (actx_cntrl.ConnectPA5('GB',dev_num)==0)
% err_msg = invoke(actx_cntrl,'GetError');
% if leng... |
7db4aefcf7692948141da643a00226a54ba7fdccc4a4c2ac2724370bce95e87f | MATLAB | 1,072 | 29 | function stats = getFalseAlarmStats(shamTrials)
%GETFALSEALARMSTATS calculates the false alarm rate from sham trials.
% Arguments:
% shamTrials - a struct array with all sham trials
% Output:
% A struct with the following fields:
% falseAlarmRate - the true false alarm rate
% adjustedFalseAlarmRate ... |
9ad874c79b1f30377db3fdacfccf12cf2a856ac24f646bf1a4623a1824d3aca7 | MATLAB | 1,077 | 43 | % function values=get_values(line,num_groups,group_num_trials,comp,crid)
% num_data=get(line,'Line_num_of_trials');
% mult=1;%multiply each value
% if ~(crid==num_groups)
% for k=crid+1:num_groups
% num=group_num_trials(k);
% mult=mult*num;
% end
% end
%
% times=1;% how many times to repeat the generation of values
% ... |
53752471040851b0a46545f47774926210b396da14f40a8cd8fffbff61d48c0f | MATLAB | 1,079 | 29 | % this function is going to interpret single spaces as regular spaces, and
% anything larger (2 or more) consecutive spaces as 'tab'
function [clean_string] = tabSplit(string_to_split)
% then we'll remove any trailing spaces
trailing_space_idx = regexp(string_to_split, '[ \t]+$');
if ~isempty(trailing_space... |
c691275994d461156af732748b20646a8cb5aa32c6a5b79b7163f5dc212c8c7b | MATLAB | 1,079 | 56 | function [img, UserSelectedCancel, filename] = ReadTiff(varargin)
UserSelectedCancel = 0;
default = cell(4,1);
for i = 1:length(varargin)
default{i} = varargin{i};
end
filename = default{1};
if isempty(filename)
[file,path] = uigetfile('.\*.tif*');
filename = fullfile(path,file);
if isequal(file,0)... |
b40d8a35a9aba0dd25043fc9f11c9c3923b50d14ee1e24ff915711a7abfb1fbd | MATLAB | 1,081 | 23 | function generatePanels_FigS6(FigS6)
%% P10 Arousal State Transitions
transNames=fieldnames(FigS6.arousalTransitions);
for transNum=1:length(transNames)
for anNum=1:size(FigS6.arousalTransitions.(transNames{transNum}).Spectrograms.FiveSecSpec,3)
emptyFlag(anNum)=max(FigS6.arousalTransitions.(tran... |
09b13a939154c71d8cf586f5f83b6a051399794941cb1d055864ecd033a0f9ef | MATLAB | 1,083 | 37 | function val=get(meta,prop_name)
% GET Get Metablock property from the specified object
% and return the value. Property names are:
% Run_mode,Line_list,Num_of_lines,Num_of_trials
if isa(prop_name,'char')
switch prop_name
case 'Run_mode'
val=meta.run_mode;
case 'Line_list'
val=meta.line_list;
case ... |
1a218788587ec136695d1c2f32c36aee13b2d1c8a5e01622739700b20c687bfb | MATLAB | 1,086 | 33 | %COLD Black-blue-cyan-white colormap
%
% Examples:
% map = cold;
% map = cold(len);
% B = cold(A);
% B = cold(A, lims);
%
% A black to white colormap through cold shades.
%
% The function can additionally be used to convert a real-valued array into
% a truecolor array using the colormap.
%
% IN:
... |
fa352cda5bc9b3ae9ebcf30ddac630de4f918505b2bd12d7fb6a8157ab8b3aa9 | MATLAB | 1,086 | 25 | function [pval, realrho, realpval, nullrho] = cs_pvalvsNull_spearman(data1,data2,permno,wsname)
%% This script was build based on the original script by Aaron Alexander-Bloch & Siyuan Liu, pvalvsNull.m, 2018-04-22
% written and edited by Christina Stier, 2022
% Calculate the p-value of correlation between two surface ... |
562721af3dd29e65398a855728da73e746f870c8f668b34b137d81a905ebbf2f | MATLAB | 1,087 | 27 | % This scripts converts t-values into partial correlatin coefficients
% (see e.g. R. Rosenthal, H. Cooper, L. Hedges, Parametric measures of effect size. The handbook of research synthesis 621, 231-244 (1994))
% Formula
% r = sign(t)*sqrt(t^2 / N - rank(M) + t^2)
% Load the results of the models (MEG markers ~ age ... |
ec9ceedba161df6dbaed85e6c20334135b9c7a2b198ae8f4dc4ef6c32911b96f | MATLAB | 1,087 | 33 | %BONE Black-blue-white colormap
%
% Examples:
% map = bone;
% map = bone(len);
% B = bone(A);
% B = bone(A, lims);
%
% Similar to MATLAB's bone function, but also able to return a concise
% colormap table.
%
% The function can additionally be used to convert a real-valued array into
% a truecolor a... |
1470e0d466924513beedfb851a7689372b80303ab83193489bd1797eacc53814 | MATLAB | 1,089 | 32 | function loc=get_relative_location(comp,comp_val)
% GET_RELATIVE_LOCATION returns the relative location of the given value
% within the range of possible values of the given component.
% LOC=GET_RELATIVE_LOCATION(COMP,COMP_VAL) returns the relative location of
% the given value (COMP_VAL) within the range of possible v... |
d445324dc7d8ff6c626a8179822e66316c414c3082dd520821c49bf28390b64e | MATLAB | 1,090 | 39 | function c = redblue(m)
%REDBLUE Shades of red and blue color map
% REDBLUE(M), is an M-by-3 matrix that defines a colormap.
% The colors begin with bright blue, range through shades of
% blue to white, and then through shades of red to bright red.
% REDBLUE, by itself, is the same length as the current... |
0b63c6d6e37eb8b1f1d0452c22ba6d817488b55458cff7cbff9bd280fbc2cbf3 | MATLAB | 1,091 | 60 | function [hh,tt,jj] = boxresample(rr,R,S,Fs,t0)
% boxresample resamples a signal with a sliding box
%
% Inputs are:
% rr: raw signal [ntr ntt]
% R: size of the box (in samples)
% S: step size (in samples)
% Fs: sampling frequency
% t0: time of first sample in raw signal
%
% Outputs:
% hh: resampled sig... |
12b86c4e4637dc15eadfcb017adbc538fbc73e43e9540c2f07fb2e164adb2f3a | MATLAB | 1,091 | 38 | function test_cam_latency()
% === Mount the camera object ====
imaqreset;
cam = videoinput('tisimaq_r2013_64', 1, 'Y800 (1280x960)');
src = getselectedsource(cam);
% === Set the parameters ====
flushdata(cam);
cam.FramesPerTrigger = 1;
cam.triggerrepeat = Inf;
src.Strobe = ... |
a4dbeee6c9b7a5ddc45c6eefaaab8074ded903ab87c6b5de93d8b16e04754d09 | MATLAB | 1,092 | 31 | function make2CalibNoiseFiles(calib, varargin)
%MAKE2CALIBNOISEFILES creates two bandpass filtered noise files.
% Arguments:
% calib - calibration structure
% dur - duration in seconds [600]
% level - target level [60]
% sF - sample frequency [192e3]
% cutoff - [4e3 60e3]
% This file depends on 'makeSomeNo... |
d3ce9c677d434c88e94b97ae380af3e252058bb0e0538675cbc61616ff8ac81b | MATLAB | 1,092 | 40 | function genBYUtoNiftiTransformFromCroppedAnalyze(in_nifti, in_crop_param_txt, out_xfm);
%this function finds the transform to go from BYU to NIFTI when the nifti
%is converted to analyze, cropped, and BYU surface generated (e.g. for the
%template surface in ComputeSurfaceDisplacements)
%in_nifti='lhipp.nii.gz';
%in... |
5f1c7fc299b640dcc52160943371061649531c48d231b4b575f8b72fefe039ac | MATLAB | 1,093 | 76 | function [P,x]=fb_peak_probability(PEAKS,varargin)
%
%
%
%
%
%
% select file to load
nparams=length(varargin);
exclude=[];
use_com=0;
range=[-inf inf];
time_bound=[0 20];
win_size=.05;
if mod(nparams,2)>0
error('Parameters must be specified as parameter/value pairs');
end
for i=1:2:nparams
switch lower(varargin... |
579611e2a27fee6dae16acc0dbbb711019cd994c0eed177b477feebd3a061963 | MATLAB | 1,099 | 32 | %PASTEL Black-pastel-white colormap
%
% Examples:
% map = pastel;
% map = pastel(len);
% B = pastel(A);
% B = pastel(A, lims);
%
% A black to white colormap with several distinct pastel shades. This
% colormap converts linearly to grayscale when printed in black & white.
%
% The function can additio... |
4e5162ef99f3c3b91b6e9102ecdabc5b0e9c380649edac438954c7fa3fa362e9 | MATLAB | 1,103 | 34 | function [bw,level]=fcmthresh(IM,sw)
%FCMTHRESH Thresholding by 3-class fuzzy c-means clustering
% [bw,level]=fcmthresh(IM,sw) outputs the binary image bw and threshold level of
% image IM using a 3-class fuzzy c-means clustering. It often works better
% than Otsu's methold which outputs larger or smaller thresh... |
18c7685b6a78f49f92e015c9df89e8606d7f940db2fb31eb35326d1912ae56aa | MATLAB | 1,105 | 33 | %HSV Red-yellow-green-cyan-blue-magenta-red colormap
%
% Examples:
% map = hsv;
% map = hsv(len);
% B = hsv(A);
% B = hsv(A, lims);
%
% Similar to MATLAB's hsv function, but also able to return a concise
% colormap table.
%
% The function can additionally be used to convert a real-valued array into
... |
bd4e8fb0bd3674fb3c48dc046df1eec5b0eb38bd8e95762574cec96872919d31 | MATLAB | 1,106 | 33 | %BRIGHT Black-bright-white colormap
%
% Examples:
% map = bright
% map = bright(len)
% B = bright(A)
% B = bright(A, lims)
%
% A black to white colormap with several distinct shades of bright color.
% This colormap converts linearly to grayscale when printed in black &
% white.
%
% The function can... |
5ab346921fdae5c12b2f87331f795c6a36675809eb0bac9982ab699f85c29be9 | MATLAB | 1,111 | 29 | function env=add_to_comp_list(env,comp_type,comp)
% ADD_TO_COMP_LIST adds a component to the given Envelope components
% list
% ENV=ADD_TO_COMP_LIST(ENV,COMP_TYPE,COMP) adds the given component
% to the given Envelope components list and the given component name to
% the given Envelope component names list. It retur... |
1b105491dff819a690f14219afd66dc505ab6a4b751a1d2ea0ee67db3a2e6b43 | MATLAB | 1,112 | 34 | function metadata = create_metadata(expdata, behavior_file_no, ...
table_no, snr_times)
out_folder = expdata.folders.out_folder_session;
AO_plot_SNR_trigs(snr_times, out_folder);
if behavior_file_no > 0
metadata.behavior_table = ...
make_behavior_table(expdata.folders.behavior, ...
expdata.exp... |
08bfebe81fe11af5b3b756750c9f9fb10a2b75f2b8a41b4fe12f7c60814573e4 | MATLAB | 1,117 | 37 | function [I, H, H_cond] = I_dis(p_past,p_joint,p_present)
%-------------------------------------------------------------------------------------------------
% PURPOSE: calculate mutual information
%
% INPUTS:
% p_past: probability distribution of past state (X^t-tau)
% joint: joint distribution of X^t (present) an... |
d29314926401fb2d32e8065865de78a7393390ecc1add03c285ba584037b92d0 | MATLAB | 1,124 | 36 | function [respMatrix, params, mResp] = makeRespMatWithConstantNoise(Npd, numRow, gain, direction, sigD, sponR, nTrials, corr, Fano, cparams1, cparams2, cparams3, cparams4, decoderN)
[mResp, params, paramsRaw] = makeMeanResp(Npd, numRow, gain, direction, sigD, sponR, cparams1, cparams2, cparams3, cparams4, decoderN);
... |
ec31416fb55b0a06c454fb778d3c6e54fa47c58a6eff8d3ffc90cbb682975858 | MATLAB | 1,128 | 27 | load("timeseries.Yeo2011.mm316.mat");
output_dir = "full_data_linear";
mkdir(output_dir);
count = 0;
for m = 1:316
subject_mx645 = corrcoef(transpose(subjects(m).mx645));
subject_mx1400 = corrcoef(transpose(subjects(m).mx1400));
subject_std2500 = corrcoef(transpose(subjects(m).std2500));
subject_mx645(2... |
3a34fe8c03dba0a05e695eb8b3e705703844802590f6ef29a28ec7ae9003ddb4 | MATLAB | 1,129 | 39 | function testDump
%TESTDUMP Test json.dump.
fixtures = {...
[], 'null';...
1, '1.0';...
inf, 'Infinity';...
-inf, '-Infinity';...
nan, 'NaN';...
true, 'true';...
'foo', 'foo';...
{}, '[]';...
struct(), '{}';...
1:5, '[1,2,... |
9a0168d8440f2af9edcfbba21a0f49ffa23af0cb4258f18a2ec17c1ce26a3051 | MATLAB | 1,129 | 29 | fields = fieldnames(fig3allbands);
fields = fields(contains(fields,'envCorr'));
bands = split(fields,'_');
bands = bands(:,2);
dataTable = struct();
maxClust = 10;
nROIs = length(fig3.ROIs);
for iBand = 1:length(fields)
thisField = fields{iBand};
thisBand = bands{iBand};
stabTable = table();
... |
38077a4fd9dc70a344979db66fab015e15680c3a1e8c5b170dc016e41dd9104a | MATLAB | 1,133 | 42 | clear
clc
behav_NE = readtable('./data/final_curves_NE_after_exclusion.csv');
behav_NM = readtable('./data/final_curves_NM_after_exclusion.csv');
eeg_NE = readmatrix('./data/EEG_NE_Cz_Grand Average Filtered.xlsx');
eeg_NM = readmatrix('./data/EEG_NM_Cz_Grand Average Filtered.xlsx');
eeg_NE(:,1) = []; eeg_NM(:... |
3ac5a7b747e8ef4fbdb40b1abc9236d9229f3e88c485501009a4ce1c907150a1 | MATLAB | 1,134 | 38 | function [result_pa5,succeeded,err]=set_atten(pa5,atten)
err='';
actx_cntrl=get(pa5,'Controler');
dev_num=get(pa5,'Device_num');
cur_atten=get(pa5,'Atten');
if atten==cur_atten
% if ~(atten==get_atten_display(pa5))
% invoke(actx_cntrl,'Display',['Att=',num2str(atten),'dB '],0);
% ... |
ed982e43f3834668b35c667f6975e8985ee0e73f8056f348633e0af329c7c136 | MATLAB | 1,135 | 30 | function [] = analyze_collage()
len = 5; % num of frames in a row of the collage
area = 3;
single_len = 200;
led_loc = [6,6];
[file_name,~] = uigetfile('*.tif','Select a Movie');
info = imfinfo(file_name);
collage_num = length(info);
frame_num = collage_num*(len.^2);
values = zeros(1... |
38b794cd2be481a8890a8394b1f637ad52db38b431e832de9a50a557b291cf36 | MATLAB | 1,136 | 30 | function [Result] = AO_AddBufferingChannel(ChannelID,SAmplingRate)
%Function used to start gathering data for the channel defined in ChannelID
%The total burffering is done for 15 sec,with the sampling rate defined in SamplingRate,therefore total samples number is 15*SAmplingRate
%ChannelID :The channel id ... |
be82559a06550561f5dede090e6ff570911177800887360a838c0ac8b920a93d | MATLAB | 1,139 | 34 | function trials = createGapStimuli(gapDurations, delays, repFactor)
%CREATEGAPSTIMULI creates an array of gap stimuli.
% Arguments:
% gapDuration - an array of gap durations
% delays - an array of delays [default: 1.25:5.25]
% repFactor - replication factor [default: 1]
%
% The factors gapDurations and delay... |
005641768da1b1165757e9a40f4cde5f8ba58515bb186ee3f080584e133c7324 | MATLAB | 1,141 | 40 | function calc_geometry(doShow) %[x, y, center_x, center_y, radius] =
load('cam_data.mat');
centData = cam_data.centData;
center_x = centData(1);
center_y = centData(2);
radius = centData(3);
areaTable = cam_data.areaTable;
len_table = areaTable.area(end);
x = radius*cos(areaTable.theta1)+center_x;
y = radius*sin(areaTa... |
cce15120f5b5be9e2aa96d25bb6541014e329780e10563d5047ec29eda91f4a8 | MATLAB | 1,141 | 46 |
clc
clear
close all
load stat_for_fig04E.mat
%% PLOT
c = lines(7);
figure('Units','normalized','OuterPosition',[.1 .1 .06 .14])
x = thresholds;
hold on
h(1) = plot_stats(x,m2,c(5,:));
h(2) = plot_stats(x,boundary,'k');
h(3) = plot_stats(x,m1,c(7,:));
xlim([4.5 15])
ylim([-20-5 50])
xlabel({'o2o threshold wrt', 'cha... |
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